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hic.wdl
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version 1.0
struct FastqPair {
File read_1
File? read_2
String? read_group
}
struct BamAndLigationCount {
File bam
File ligation_count
Boolean single_ended
}
struct RuntimeEnvironment {
String docker
String singularity
}
workflow hic {
meta {
version: "1.15.1"
caper_docker: "encodedcc/hic-pipeline:1.15.1"
caper_singularity: "docker://encodedcc/hic-pipeline:1.15.1"
croo_out_def: "https://raw.githubusercontent.com/ENCODE-DCC/hic-pipeline/dev/croo_out_def.json"
description: "ENCODE Hi-C pipeline, see https://github.com/ENCODE-DCC/hic-pipeline for details."
}
input {
# Main entrypoint, need to specify all five of these values except read_groups when running from fastqs
Array[Array[FastqPair]] fastq = []
Array[String] restriction_enzymes = []
String? ligation_site_regex
File? restriction_sites
File? chrsz
File? reference_index
# Entrypoint for loop and TAD calls
File? input_hic
# Parameters controlling delta calls
Boolean no_delta = false
# Parameters
Boolean intact = false
Array[String] normalization_methods = []
Array[Int] create_hic_in_situ_resolutions = [2500000, 1000000, 500000, 250000, 100000, 50000, 25000, 10000, 5000, 2000, 1000, 500, 200, 100]
Array[Int] create_hic_intact_resolutions = [2500000, 1000000, 500000, 250000, 100000, 50000, 25000, 10000, 5000, 2000, 1000, 500, 200, 100, 50, 20, 10]
# Feature flags
Boolean no_pairs = false
Boolean no_call_loops = false
Boolean no_call_tads = false
Boolean no_eigenvectors = false
Boolean no_slice = false
# Resource parameters
Int align_num_cpus = 32
Int align_ram_gb_in_situ = 64
Int align_ram_gb_intact = 88
Int align_disk_size_gb_in_situ = 1000
Int align_disk_size_gb_intact = 1500
Int chimeric_sam_nonspecific_disk_size_gb = 7000
Int chimeric_sam_specific_disk_size_gb = 1500
Int dedup_ram_gb_in_situ = 32
Int dedup_ram_gb_intact = 48
Int dedup_disk_size_gb_in_situ = 5000
Int dedup_disk_size_gb_intact = 7500
Int? create_hic_num_cpus
Int? create_hic_ram_gb
Int? create_hic_juicer_tools_heap_size_gb
Int? create_hic_disk_size_gb
Int? add_norm_num_cpus
Int? add_norm_ram_gb
Int? add_norm_disk_size_gb
Int? create_accessibility_track_ram_gb
Int? create_accessibility_track_disk_size_gb
String assembly_name = "undefined"
String docker = "encodedcc/hic-pipeline:1.15.1"
String singularity = "docker://encodedcc/hic-pipeline:1.15.1"
String delta_docker = "encodedcc/hic-pipeline:1.15.1_delta"
String hiccups_docker = "encodedcc/hic-pipeline:1.15.1_hiccups"
}
RuntimeEnvironment runtime_environment = {
"docker": docker,
"singularity": singularity
}
RuntimeEnvironment hiccups_runtime_environment = {
"docker": hiccups_docker,
"singularity": singularity
}
RuntimeEnvironment delta_runtime_environment = {
"docker": delta_docker,
"singularity": singularity
}
Int align_ram_gb = if intact then align_ram_gb_intact else align_ram_gb_in_situ
Int align_disk_size_gb = if intact then align_disk_size_gb_intact else align_disk_size_gb_in_situ
Int dedup_ram_gb = if intact then dedup_ram_gb_intact else dedup_ram_gb_in_situ
Int dedup_disk_size_gb = if intact then dedup_disk_size_gb_intact else dedup_disk_size_gb_in_situ
String delta_models_path = if intact then "ultimate-models" else "beta-models"
Array[Int] delta_resolutions = if intact then [5000, 2000, 1000] else [5000, 10000]
Array[Int] create_hic_resolutions = if intact then create_hic_intact_resolutions else create_hic_in_situ_resolutions
# Default MAPQ thresholds for generating .hic contact maps
Array[Int] DEFAULT_HIC_QUALITIES = [1, 30]
Boolean is_nonspecific = length(restriction_enzymes) > 0 && restriction_enzymes[0] == "none"
if (!defined(input_hic)) {
if (!defined(ligation_site_regex)) {
call get_ligation_site_regex { input:
restriction_enzymes = restriction_enzymes,
runtime_environment = runtime_environment,
}
}
String ligation_site = select_first([ligation_site_regex, get_ligation_site_regex.ligation_site_regex])
if (!is_nonspecific && !defined(restriction_sites)) {
call exit_early { input:
message = "Must provide restriction sites file if enzyme is not `none`",
runtime_environment = runtime_environment,
}
}
}
call normalize_assembly_name { input:
assembly_name = assembly_name,
runtime_environment = runtime_environment,
}
scatter(i in range(length(fastq))) {
Array[FastqPair] replicate = fastq[i]
scatter(fastq_pair in replicate) {
call align { input:
fastq_pair = fastq_pair,
idx_tar = select_first([reference_index]),
ligation_site = select_first([ligation_site]),
num_cpus = align_num_cpus,
ram_gb = align_ram_gb,
disk_size_gb = align_disk_size_gb,
runtime_environment = runtime_environment,
}
}
if (is_nonspecific) {
scatter(bam_and_ligation_count in align.bam_and_ligation_count) {
call chimeric_sam_nonspecific { input:
bam = bam_and_ligation_count.bam,
ligation_count = bam_and_ligation_count.ligation_count,
single_ended = bam_and_ligation_count.single_ended,
disk_size_gb = chimeric_sam_nonspecific_disk_size_gb,
runtime_environment = runtime_environment,
}
}
}
if (!is_nonspecific) {
scatter(bam_and_ligation_count in align.bam_and_ligation_count) {
call chimeric_sam_specific { input:
bam = bam_and_ligation_count.bam,
ligation_count = bam_and_ligation_count.ligation_count,
restriction_sites = select_first([restriction_sites]),
single_ended = bam_and_ligation_count.single_ended,
disk_size_gb = chimeric_sam_specific_disk_size_gb,
runtime_environment = runtime_environment,
}
}
}
call merge { input:
bams = flatten(
select_all(
[
chimeric_sam_specific.output_bam,
chimeric_sam_nonspecific.output_bam,
]
)
),
output_bam_filename = "merged_" + i,
runtime_environment = runtime_environment,
}
call dedup { input:
bam = merge.bam,
ram_gb = dedup_ram_gb,
disk_size_gb = dedup_disk_size_gb,
runtime_environment = runtime_environment,
}
call bam_to_pre as bam_to_pre_for_stats { input:
bam = dedup.deduped_bam,
quality = 1,
output_filename_suffix = "_lib" + i,
runtime_environment = runtime_environment,
}
call calculate_stats as calculate_stats_on_library { input:
alignment_stats = flatten(
select_all([chimeric_sam_specific.stats, chimeric_sam_nonspecific.stats])
),
bam = dedup.deduped_bam,
pre = bam_to_pre_for_stats.pre,
restriction_sites = restriction_sites,
chrom_sizes = select_first([chrsz]),
ligation_site = select_first([ligation_site]),
output_filename_suffix = "_lib" + i,
single_ended = align.bam_and_ligation_count[0].single_ended,
runtime_environment = runtime_environment,
}
}
if (!defined(input_hic)) {
call merge as merge_replicates { input:
bams = dedup.deduped_bam,
runtime_environment = runtime_environment,
}
# convert alignable bam to pairs to be consistent with 4DN
if ( !no_pairs && defined(chrsz)) {
call bam_to_pre as bam_to_pre_mapq0 { input:
bam = merge_replicates.bam,
quality = 0,
runtime_environment = runtime_environment,
}
call pre_to_pairs { input:
pre = bam_to_pre_mapq0.pre,
chrom_sizes = select_first([chrsz]),
runtime_environment = runtime_environment,
}
}
}
Array[Int] qualities = if !defined(input_hic) then DEFAULT_HIC_QUALITIES else []
scatter(i in range(length(qualities))) {
call bam_to_pre { input:
bam = select_first([merge_replicates.bam]),
quality = qualities[i],
runtime_environment = runtime_environment,
}
if (intact && qualities[i] == 30) {
call create_accessibility_track { input:
pre = bam_to_pre.pre,
chrom_sizes = select_first([chrsz]),
ram_gb = create_accessibility_track_ram_gb,
disk_size_gb = create_accessibility_track_disk_size_gb,
runtime_environment = runtime_environment,
}
}
call calculate_stats { input:
alignment_stats = flatten(
select_all(
flatten(
[chimeric_sam_specific.stats, chimeric_sam_nonspecific.stats]
)
)
),
bam = select_first([merge_replicates.bam]),
pre = bam_to_pre.pre,
restriction_sites = restriction_sites,
chrom_sizes = select_first([chrsz]),
ligation_site = select_first([ligation_site]),
quality = qualities[i],
single_ended = align.bam_and_ligation_count[0][0].single_ended,
runtime_environment = runtime_environment,
}
# If Juicer Tools doesn't support the assembly then need to pass chrom sizes
if (!normalize_assembly_name.assembly_is_supported) {
call create_hic as create_hic_with_chrom_sizes { input:
pre = bam_to_pre.pre,
pre_index = bam_to_pre.index,
chrsz = select_first([chrsz]),
restriction_sites = restriction_sites,
quality = qualities[i],
stats = calculate_stats.stats,
stats_hists = calculate_stats.stats_hists,
resolutions = create_hic_resolutions,
assembly_name = assembly_name,
num_cpus = create_hic_num_cpus,
ram_gb = create_hic_ram_gb,
juicer_tools_heap_size_gb = create_hic_juicer_tools_heap_size_gb,
disk_size_gb = create_hic_disk_size_gb,
runtime_environment = runtime_environment,
}
}
if (normalize_assembly_name.assembly_is_supported) {
call create_hic { input:
pre = bam_to_pre.pre,
pre_index = bam_to_pre.index,
restriction_sites = restriction_sites,
quality = qualities[i],
stats = calculate_stats.stats,
stats_hists = calculate_stats.stats_hists,
resolutions = create_hic_resolutions,
assembly_name = normalize_assembly_name.normalized_assembly_name,
num_cpus = create_hic_num_cpus,
ram_gb = create_hic_ram_gb,
juicer_tools_heap_size_gb = create_hic_juicer_tools_heap_size_gb,
disk_size_gb = create_hic_disk_size_gb,
runtime_environment = runtime_environment,
}
}
File unnormalized_hic_file = select_first([
if (defined(create_hic.output_hic))
then create_hic.output_hic
else create_hic_with_chrom_sizes.output_hic
])
call add_norm { input:
hic = unnormalized_hic_file,
normalization_methods = normalization_methods,
quality = qualities[i],
num_cpus = add_norm_num_cpus,
ram_gb = add_norm_ram_gb,
disk_size_gb = add_norm_disk_size_gb,
runtime_environment = runtime_environment,
}
if (!no_call_tads) {
call arrowhead { input:
hic_file = add_norm.output_hic,
quality = qualities[i],
runtime_environment = runtime_environment,
}
}
if (!no_call_loops) {
if (!intact) {
call hiccups { input:
hic_file = add_norm.output_hic,
quality = qualities[i],
runtime_environment = hiccups_runtime_environment,
}
}
if (intact) {
call hiccups_2 { input:
hic = add_norm.output_hic,
quality = qualities[i],
runtime_environment = hiccups_runtime_environment,
}
call localizer as localizer_intact { input:
hic = add_norm.output_hic,
loops = hiccups_2.merged_loops,
quality = qualities[i],
runtime_environment = runtime_environment,
}
}
}
if (defined(chrsz) && !no_eigenvectors) {
call create_eigenvector { input:
hic_file = add_norm.output_hic,
chrom_sizes = select_first([chrsz]),
output_filename_suffix = "_" + qualities[i],
runtime_environment = runtime_environment,
}
call create_eigenvector as create_eigenvector_10kb { input:
hic_file = add_norm.output_hic,
chrom_sizes = select_first([chrsz]),
resolution = 10000,
output_filename_suffix = "_" + qualities[i],
runtime_environment = runtime_environment,
}
}
}
if (!no_delta) {
call delta { input:
# Only run delta on MAPQ >= 30
hic = if length(add_norm.output_hic) > 1 then add_norm.output_hic[1] else select_first([input_hic]),
resolutions = delta_resolutions,
models_path = delta_models_path,
runtime_environment = delta_runtime_environment,
}
call localizer as localizer_delta { input:
hic = if length(add_norm.output_hic) > 1 then add_norm.output_hic[1] else select_first([input_hic]),
loops = delta.loops,
runtime_environment = runtime_environment,
}
}
if (defined(input_hic)) {
if (!no_call_tads) {
call arrowhead as arrowhead_input_hic { input:
hic_file = select_first([input_hic]),
runtime_environment = runtime_environment,
}
}
if (!no_call_loops) {
if (!intact) {
call hiccups as hiccups_input_hic { input:
hic_file = select_first([input_hic]),
runtime_environment = hiccups_runtime_environment,
}
}
if (intact) {
call hiccups_2 as hiccups_2_input_hic { input:
hic = select_first([input_hic]),
runtime_environment = hiccups_runtime_environment,
}
call localizer as localizer_intact_input_hic { input:
hic = select_first([input_hic]),
loops = hiccups_2_input_hic.merged_loops,
runtime_environment = runtime_environment,
}
}
}
}
if (!no_slice) {
File hic_file = if length(add_norm.output_hic) > 1 then add_norm.output_hic[1] else select_first([input_hic])
call slice as slice_25kb { input:
hic_file = hic_file,
resolution = 25000,
runtime_environment = runtime_environment,
}
call slice as slice_50kb { input:
hic_file = hic_file,
resolution = 50000,
runtime_environment = runtime_environment,
}
call slice as slice_100kb { input:
hic_file = hic_file,
resolution = 100000,
runtime_environment = runtime_environment,
}
}
}
task get_ligation_site_regex {
input {
Array[String] restriction_enzymes
RuntimeEnvironment runtime_environment
}
String output_path = "ligation_site_regex.txt"
command <<<
set -euo pipefail
python3 "$(which get_ligation_site_regex.py)" \
--enzymes ~{sep=" " restriction_enzymes} \
--outfile ~{output_path}
>>>
output {
String ligation_site_regex = read_string("~{output_path}")
# Surface the original file for testing purposes
File ligation_site_regex_file = "~{output_path}"
}
runtime {
cpu : "1"
memory: "500 MB"
docker: runtime_environment.docker
singularity: runtime_environment.singularity
}
}
task normalize_assembly_name {
input {
String assembly_name
String normalized_assembly_name_output_path = "normalized_assembly_name.txt"
String assembly_is_supported_output_path = "is_supported.txt"
RuntimeEnvironment runtime_environment
}
command <<<
set -euo pipefail
python3 "$(which normalize_assembly_name.py)" \
~{assembly_name} \
~{normalized_assembly_name_output_path} \
~{assembly_is_supported_output_path}
>>>
output {
String normalized_assembly_name = read_string("~{normalized_assembly_name_output_path}")
Boolean assembly_is_supported = read_boolean("~{assembly_is_supported_output_path}")
}
runtime {
cpu : "1"
memory: "500 MB"
docker: runtime_environment.docker
singularity: runtime_environment.singularity
}
}
task align {
input {
FastqPair fastq_pair
File idx_tar # reference bwa index tar
String ligation_site
Int num_cpus = 32
Int ram_gb = 64
Int disk_size_gb = 1000
RuntimeEnvironment runtime_environment
}
command {
set -euo pipefail
echo "Starting align"
mkdir reference
cd reference && tar -xvf ${idx_tar}
index_folder=$(ls)
reference_fasta=$(ls | head -1)
reference_folder=$(pwd)
reference_index_path=$reference_folder/$reference_fasta
cd ..
usegzip=1
name="result"
ligation="${ligation_site}"
name1=${fastq_pair.read_1}
name2=${fastq_pair.read_2}
ext=""
singleend=~{if(defined(fastq_pair.read_2)) then "0" else "1"}
#count ligations
# Need to unset the -e option, when ligation site is XXXX grep will exit with
# non-zero status
set +e
source /opt/scripts/common/countligations.sh
set -e
# Align reads
echo "Running bwa command"
bwa \
mem \
~{if defined(fastq_pair.read_2) then "-SP5M" else "-5M"} \
~{if defined(fastq_pair.read_group) then "-R '" + fastq_pair.read_group + "'" else ""} \
-t ~{num_cpus} \
-K 320000000 \
$reference_index_path \
${fastq_pair.read_1} \
~{default="" fastq_pair.read_2} | \
samtools view -hbS - > aligned.bam
mv result_norm.txt.res.txt ligation_count.txt
}
output {
BamAndLigationCount bam_and_ligation_count = object {
bam: "aligned.bam",
ligation_count: "ligation_count.txt",
single_ended: length(select_all([fastq_pair.read_2])) == 0,
}
}
runtime {
cpu : "~{num_cpus}"
memory: "~{ram_gb} GB"
disks: "local-disk ~{disk_size_gb} HDD"
docker: runtime_environment.docker
singularity: runtime_environment.singularity
}
}
task chimeric_sam_specific {
input {
File bam
File ligation_count
File restriction_sites
Boolean single_ended
Int num_cpus = 8
Int ram_gb = 16
Int disk_size_gb = 1000
RuntimeEnvironment runtime_environment
}
command <<<
set -euo pipefail
RESTRICTION_SITES_FILENAME=restriction_sites.txt
gzip -dc ~{restriction_sites} > $RESTRICTION_SITES_FILENAME
cp ~{ligation_count} result_norm.txt.res.txt
samtools view -h -@ ~{num_cpus - 1} ~{bam} > result.sam
awk \
-v stem=result_norm \
-v site_file=$RESTRICTION_SITES_FILENAME \
~{if(single_ended) then "-v singleend=1" else ""} \
-f "$(which chimeric_sam.awk)" \
result.sam | \
samtools sort -t cb -n --threads ~{num_cpus} > chimeric_sam_specific.bam
>>>
output {
File output_bam = "chimeric_sam_specific.bam"
File stats = "result_norm.txt.res.txt"
}
runtime {
cpu : "~{num_cpus}"
disks: "local-disk ~{disk_size_gb} HDD"
memory: "~{ram_gb} GB"
docker: runtime_environment.docker
singularity: runtime_environment.singularity
}
}
task chimeric_sam_nonspecific {
input {
File bam
File ligation_count
Boolean single_ended
Int num_cpus = 8
Int ram_gb = 16
Int disk_size_gb = 1000
RuntimeEnvironment runtime_environment
}
command <<<
set -euo pipefail
cp ~{ligation_count} result_norm.txt.res.txt
samtools view -h -@ ~{num_cpus - 1} ~{bam} > result.sam
awk \
-v stem=result_norm \
~{if(single_ended) then "-v singleend=1" else ""} \
-f "$(which chimeric_sam.awk)" \
result.sam > result.sam2
~{if(single_ended) then "samtools sort -t cb -n --threads " + num_cpus + " result.sam2 > chimeric_sam_nonspecific.bam && exit 0" else ""}
awk \
-v avgInsertFile=result_norm.txt.res.txt \
-f "$(which adjust_insert_size.awk)" \
result.sam2 | \
samtools sort -t cb -n --threads ~{num_cpus} > chimeric_sam_nonspecific.bam
>>>
output {
File output_bam = "chimeric_sam_nonspecific.bam"
File stats = "result_norm.txt.res.txt"
}
runtime {
cpu : "~{num_cpus}"
memory: "~{ram_gb} GB"
disks: "local-disk ~{disk_size_gb} HDD"
docker: runtime_environment.docker
singularity: runtime_environment.singularity
}
}
task merge {
input {
Array[File] bams
Int num_cpus = 8
Int ram_gb = 16
Int disk_size_gb = 6000
String output_bam_filename = "merged"
RuntimeEnvironment runtime_environment
}
command <<<
set -euo pipefail
samtools merge \
-c \
-t cb \
-n \
--threads ~{num_cpus - 1} \
~{output_bam_filename}.bam \
~{sep=' ' bams}
>>>
output {
File bam = "~{output_bam_filename}.bam"
}
runtime {
cpu : "~{num_cpus}"
memory: "~{ram_gb} GB"
disks: "local-disk ~{disk_size_gb} HDD"
docker: runtime_environment.docker
singularity: runtime_environment.singularity
}
}
task dedup {
input {
File bam
Int num_cpus = 8
Int ram_gb = 32
Int disk_size_gb = 5000
RuntimeEnvironment runtime_environment
}
command <<<
set -euo pipefail
samtools view \
-h \
-@ ~{num_cpus - 1} \
~{bam} | \
awk -f "$(which dups_sam.awk)" > merged_dedup.sam
samtools view -b -@ ~{num_cpus - 1} merged_dedup.sam > merged_dedup.bam
>>>
output {
File deduped_bam = "merged_dedup.bam"
}
runtime {
cpu : "~{num_cpus}"
memory: "~{ram_gb} GB"
disks: "local-disk ~{disk_size_gb} HDD"
docker: runtime_environment.docker
singularity: runtime_environment.singularity
}
}
task pre_to_pairs {
input {
File pre
File chrom_sizes
RuntimeEnvironment runtime_environment
}
command {
set -euo pipefail
PRE_FILENAME=pre.txt
gzip -dc ~{pre} > $PRE_FILENAME
perl "$(which juicer_shortform2pairs.pl)" $PRE_FILENAME ~{chrom_sizes} pairix
}
output {
File out_file = "pairix.bsorted.pairs.gz"
}
runtime {
cpu : "8"
memory: "16 GB"
disks: "local-disk 3000 HDD"
docker: runtime_environment.docker
singularity: runtime_environment.singularity
}
}
task bam_to_pre {
input {
File bam
Int quality
Int num_cpus = 8
String output_filename_suffix = ""
RuntimeEnvironment runtime_environment
}
command <<<
set -euo pipefail
MERGED_NODUPS_FILENAME=merged_nodups_~{quality}~{output_filename_suffix}.txt
MERGED_NODUPS_INDEX_FILENAME=merged_nodups_~{quality}~{output_filename_suffix}_index.txt
samtools view \
-h \
-F 1024 \
-O sam \
~{bam} \
-@ ~{num_cpus - 1} | \
awk -v mapq=~{quality} -f "$(which sam_to_pre.awk)" > $MERGED_NODUPS_FILENAME
$(which index_by_chr.awk) $MERGED_NODUPS_FILENAME 500000 > $MERGED_NODUPS_INDEX_FILENAME
gzip -n $MERGED_NODUPS_FILENAME
gzip -n $MERGED_NODUPS_INDEX_FILENAME
>>>
output {
File pre = "merged_nodups_~{quality}~{output_filename_suffix}.txt.gz"
File index = "merged_nodups_~{quality}~{output_filename_suffix}_index.txt.gz"
}
runtime {
cpu : "~{num_cpus}"
disks: "local-disk 3000 HDD"
memory : "64 GB"
docker: runtime_environment.docker
singularity: runtime_environment.singularity
}
}
task calculate_stats {
input {
Array[File] alignment_stats
File pre
File chrom_sizes
File bam
File? restriction_sites
String ligation_site
String output_filename_suffix = ""
Boolean single_ended = false
Int quality = 0
RuntimeEnvironment runtime_environment
}
command <<<
PRE_FILE=pre.txt
RESTRICTION_SITES_FILENAME=restriction_sites.txt
STATS_FILENAME=stats_~{quality}~{output_filename_suffix}.txt
gzip -dc ~{pre} > $PRE_FILE
~{if defined(restriction_sites) then "gzip -dc " + restriction_sites + " > $RESTRICTION_SITES_FILENAME" else ""}
if [ ~{if(single_ended) then "1" else "0"} -eq 1 ]
then
RET=$(samtools view -f 1024 -F 256 ~{bam} | awk '{if ($0~/rt:A:7/){singdup++}else{dup++}}END{print dup,singdup}')
DUPS=$(echo $RET | awk '{print $1}')
SINGDUPS=$(echo $RET | awk '{print $2}')
awk \
-f "$(which stats_sub.awk)" \
-v dups=$DUPS \
-v singdups=$SINGDUPS \
-v ligation="~{ligation_site}" \
-v singleend=1 \
~{sep=" " alignment_stats} >> $STATS_FILENAME
else
DUPS=$(samtools view -c -f 1089 -F 256 ~{bam})
awk \
-f "$(which stats_sub.awk)" \
-v dups=$DUPS \
-v ligation=$ligation \
~{sep=" " alignment_stats} >> $STATS_FILENAME
fi
java \
-Ddevelopment=false \
-Djava.awt.headless=true \
-Xmx16g \
-jar /opt/scripts/common/juicer_tools.jar \
statistics \
~{if defined(restriction_sites) then "$RESTRICTION_SITES_FILENAME" else "none"} \
$STATS_FILENAME \
~{pre} \
~{chrom_sizes}
python3 \
"$(which jsonify_stats.py)" \
$STATS_FILENAME \
stats_~{quality}~{output_filename_suffix}.json
>>>
output {
File stats = "stats_~{quality}~{output_filename_suffix}.txt"
File stats_json = "stats_~{quality}~{output_filename_suffix}.json"
File stats_hists = "stats_~{quality}~{output_filename_suffix}_hists.m"
}
runtime {
cpu : "1"
disks: "local-disk 4000 HDD"
memory : "16 GB"
docker: runtime_environment.docker
singularity: runtime_environment.singularity
}
}
task create_hic {
input {
File pre
File pre_index
File stats
File stats_hists
Int quality
Array[Int] resolutions
String? assembly_name
File? chrsz
File? restriction_sites
Int num_cpus = 16
# Should always set juicer_tools_heap_size_gb < ram_gb
Int ram_gb = 384
Int juicer_tools_heap_size_gb = 370
Int disk_size_gb = 2000
RuntimeEnvironment runtime_environment
}
command <<<
set -euo pipefail
PRE_FILE=pre.txt
PRE_INDEX_FILE=pre_index.txt
RESTRICTION_SITES_FILENAME=restriction_sites.txt
gzip -dc ~{pre} > $PRE_FILE
gzip -dc ~{pre_index} > $PRE_INDEX_FILE
~{if defined(restriction_sites) then "gzip -dc " + restriction_sites + " > $RESTRICTION_SITES_FILENAME" else ""}
# If the assembly name is empty, then we write chrsz path into file as usual, otherwise, use the assembly name instead of the path
java \
-Ddevelopment=false \
-Djava.awt.headless=true \
-Xmx~{juicer_tools_heap_size_gb}g \
-jar /opt/scripts/common/juicer_tools.jar \
pre \
-n \
~{if defined(restriction_sites) then "-f $RESTRICTION_SITES_FILENAME" else ""} \
-s ~{stats} \
-g ~{stats_hists} \
~{if defined(assembly_name) then "-y " + assembly_name else ""} \
-r ~{sep="," resolutions} \
-i $PRE_INDEX_FILE \
--block-capacity 1000000 \
--threads ~{num_cpus} \
$PRE_FILE \
inter_~{quality}_unnormalized.hic \
~{if defined(chrsz) then chrsz else assembly_name}
>>>
output {
File output_hic = "inter_~{quality}_unnormalized.hic"
}
runtime {
cpu : "~{num_cpus}"
memory : "~{ram_gb} GB"
disks: "local-disk ~{disk_size_gb} HDD"
docker: runtime_environment.docker
singularity: runtime_environment.singularity
}
}
task add_norm {
input {
File hic
Array[String] normalization_methods = []
Int? mthreads #only used with addnorm2
Int? save_ram #only used with addnorm2
Int quality
Int num_cpus = 24
Int disk_size_gb = 256
Int ram_gb = 72
String juicer_tools_jar = "/opt/scripts/common/juicer_tools.jar"
String normalization_command = "addNorm"
RuntimeEnvironment runtime_environment
}
Int java_heap_gb = ram_gb - 12
command {
set -euo pipefail
cp ~{hic} inter_~{quality}.hic
java \
-Ddevelopment=false \
-Djava.awt.headless=true \
-Xmx~{if java_heap_gb > 0 then java_heap_gb else 12}g \
-jar ~{juicer_tools_jar} \
~{normalization_command} \
~{if length(normalization_methods) > 0 then "-k" else ""} ~{sep="," normalization_methods} \
~{"--mthreads" + mthreads} \
~{"--save-ram" + save_ram} \
--threads ~{num_cpus} \
inter_~{quality}.hic
}
output {
File output_hic = "inter_~{quality}.hic"
}
runtime {
cpu : "~{num_cpus}"
disks: "local-disk ~{disk_size_gb} HDD"
memory : "~{ram_gb} GB"
docker: runtime_environment.docker
singularity: runtime_environment.singularity
}
}
task arrowhead {
input {
File hic_file
Int disk_size_gb = 100
Int num_cpus = 1
Int ram_gb = 32
Int quality = 0
RuntimeEnvironment runtime_environment
}
command <<<
set -euo pipefail
java \
-Ddevelopment=false \
-Djava.awt.headless=true \
-Xmx16g \
-jar /opt/scripts/common/juicer_tools.jar \
arrowhead \
~{hic_file} \
contact_domains
gzip -n contact_domains/*
STEM=$(basename contact_domains/*.bedpe.gz .bedpe.gz)
mv contact_domains/*.bedpe.gz "${STEM}_~{quality}.bedpe.gz"
>>>
output {
File out_file = glob('*_~{quality}.bedpe.gz')[0]
}
runtime {
cpu : "~{num_cpus}"
disks: "local-disk ~{disk_size_gb} HDD"
memory : "~{ram_gb} GB"
docker: runtime_environment.docker
singularity: runtime_environment.singularity
}